GREMLIN Database
YFDO - Putative uncharacterized protein YfdO
UniProt: P0AD35 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG14137
Length: 122 (94)
Sequences: 104 (86)
Seq/√Len: 8.9

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
38_N42_L3.6750.97
41_R45_V2.7630.86
11_I73_S2.6230.83
67_W80_K2.5770.81
76_K79_E2.4550.78
43_M54_I2.4470.78
58_Y61_V2.3950.76
38_N41_R2.2310.71
49_R82_D2.1220.67
42_L46_Q1.9670.61
2_T9_K1.9450.60
66_F73_S1.9050.58
59_S63_R1.8810.57
76_K80_K1.8290.55
5_Q30_E1.7590.52
57_M88_L1.7180.50
47_D82_D1.7120.50
55_C81_W1.6110.45
55_C58_Y1.5880.44
29_K32_N1.5860.44
50_T54_I1.5330.42
32_N35_A1.4920.40
7_L58_Y1.4720.40
2_T26_V1.4220.37
83_E87_R1.3840.36
11_I27_R1.3550.35
43_M74_P1.3380.34
48_G89_S1.3180.33
45_V75_S1.2530.31
24_E31_P1.2240.30
10_K96_T1.2160.30
7_L80_K1.2150.30
97_E100_E1.1900.29
40_I59_S1.1640.28
2_T8_W1.1530.27
60_R88_L1.1090.26
6_W44_C1.1070.26
61_V71_V1.1010.26
70_N73_S1.1010.26
6_W51_H1.1010.26
53_Q84_L1.0870.25
45_V92_V1.0860.25
14_L53_Q1.0860.25
49_R57_M1.0730.25
66_F78_R1.0680.25
61_V87_R1.0160.23
9_K79_E1.0100.23
43_M87_R1.0000.22
15_Y23_G0.9720.22
38_N51_H0.9610.21
5_Q13_A0.9440.21
64_D87_R0.9330.20
64_D84_L0.9040.20
6_W55_C0.8970.20
40_I88_L0.8920.19
90_P94_T0.8900.19
39_E64_D0.8800.19
48_G52_K0.8750.19
37_A80_K0.8510.18
33_W58_Y0.8470.18
73_S78_R0.8400.18
8_W82_D0.8350.18
75_S93_S0.8330.18
11_I72_L0.8260.18
53_Q87_R0.8230.18
51_H55_C0.8150.17
63_R68_C0.8140.17
31_P41_R0.8030.17
10_K46_Q0.8030.17
80_K83_E0.7970.17
61_V83_E0.7940.17
40_I43_M0.7890.17
7_L59_S0.7800.17
25_V61_V0.7760.16
67_W71_V0.7730.16
8_W28_P0.7710.16
11_I15_Y0.7680.16
57_M72_L0.7620.16
57_M87_R0.7600.16
7_L82_D0.7580.16
29_K50_T0.7370.16
91_S97_E0.7350.15
33_W37_A0.7300.15
58_Y62_S0.7300.15
38_N74_P0.7280.15
66_F70_N0.7170.15
47_D70_N0.7170.15
44_C63_R0.7150.15
38_N54_I0.6960.15
43_M49_R0.6920.15
86_L100_E0.6870.14
87_R90_P0.6830.14
44_C51_H0.6830.14
45_V96_T0.6810.14
37_A67_W0.6770.14
57_M62_S0.6720.14
48_G60_R0.6620.14
73_S76_K0.6590.14
47_D66_F0.6590.14
56_E63_R0.6520.14
38_N44_C0.6510.14
43_M50_T0.6500.14
68_C94_T0.6430.14
71_V86_L0.6400.13
4_A84_L0.6370.13
10_K28_P0.6370.13
44_C81_W0.6260.13
51_H81_W0.6250.13
38_N43_M0.6230.13
2_T62_S0.6170.13
50_T63_R0.6120.13
30_E102_P0.6120.13
42_L50_T0.6100.13
60_R87_R0.6070.13
72_L76_K0.6060.13
39_E60_R0.6030.13
23_G80_K0.6000.13
75_S91_S0.5980.13
3_C10_K0.5980.13
95_Y100_E0.5900.12
26_V60_R0.5830.12
9_K45_V0.5800.12
6_W81_W0.5800.12
30_E85_S0.5800.12
11_I75_S0.5770.12
46_Q86_L0.5770.12
40_I97_E0.5750.12
9_K92_V0.5650.12
13_A71_V0.5610.12
92_V97_E0.5470.12
66_F74_P0.5460.12
3_C7_L0.5430.12
68_C88_L0.5360.11
74_P79_E0.5310.11
61_V64_D0.5260.11
8_W15_Y0.5220.11
15_Y49_R0.5150.11
9_K101_D0.5120.11
30_E34_T0.5110.11
91_S102_P0.5040.11
76_K83_E0.5000.11
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
2ru8A 1 0.6885 87.6 0.901 Contact Map
3sciE 1 0.6311 11.6 0.947 Contact Map
1e0bA 2 0.5164 4.7 0.955 Contact Map
3sbtB 1 0.5574 4.2 0.956 Contact Map
2l96X 1 0.1967 4 0.957 Contact Map
1wfiA 1 0.3852 2.6 0.961 Contact Map
3qb5K 2 0.7459 2.6 0.961 Contact Map
3qryB 1 0.4098 2.6 0.961 Contact Map
3ro3B 1 0.1311 2.5 0.961 Contact Map
2lkqA 1 0.1967 2.5 0.961 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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